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bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ

Description:
bGalGal1 paternal white leghorn layer GRCg7w with chromosomes W and Z
Organism name:
Gallus gallus (chicken)
Infraspecific name:
Breed: Cross of Broiler mother + white leghorn layer father
Isolate:
bGalGal1
Sex:
female
BioSample:
SAMN15960293
BioProject:
PRJNA660758
Submitter:
Vertebrate Genomes Project
Date:
2021/10/01
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_016700215.2 (latest)
RefSeq assembly accession:
GCF_016700215.2 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAENSL01
Assembly method:
TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. SMRTLink7.0.1; Freebayes v. 1.3.1; gEVAL manual curation v. 2020-07-09; VGP trio assembly pipeline v. 1.6
Expected final version:
no
Genome coverage:
102.01x
Sequencing technology:
PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS

IDs: 11036911 [UID] 29164768 [GenBank] 30673228 [RefSeq]

See Genome Information for Gallus gallus

Pathogen Detection Resources

There are 39 assemblies for this organism

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History (Show revision history)

Comment

Contigs JAENSL010000510-JAENSL010000685 were added to the assembly in September 2021. They are copies of the sequences of the sex chromosomes W and Z from the corresponding maternal haplotype assembly JAENSK000000000 (bGalGal1.mat.broiler.GRCg7b, GCA_016699485.1). Therefore, this updated assembly bGalGal1.pat.whiteleghornlayer.GRCg7w_WZ (GCA_016700215.2) represents ... the male/paternal haplotype assembly plus the female/maternal haplotype assembly's sex chromosomes.  more

Global statistics

Total sequence length1,050,511,239
Total ungapped length1,046,014,928
Gaps between scaffolds0
Number of scaffolds276
Scaffold N5090,563,926
Scaffold L504
Number of contigs685
Contig N5017,744,542
Contig L5018
Total number of chromosomes and plasmids41
Number of component sequences (WGS or clone)685

Supplemental Content

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Assembly Information

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCF_016700225.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM028523.1=NC_052573.12
Chromosome 2CM028524.1=NC_052574.10
Chromosome 3CM028525.1=NC_052575.10
Chromosome 4CM028526.1=NC_052576.11
Chromosome 5CM028527.1=NC_052577.15
Chromosome 6CM028528.1=NC_052578.10
Chromosome 7CM028529.1=NC_052579.11
Chromosome 8CM028530.1=NC_052580.12
Chromosome 9CM028531.1=NC_052581.12
Chromosome 10CM028532.1=NC_052582.12
Chromosome 11CM028533.1=NC_052583.10
Chromosome 12CM028534.1=NC_052584.10
Chromosome 13CM028535.1=NC_052585.10
Chromosome 14CM028536.1=NC_052586.10
Chromosome 15CM028537.1=NC_052587.10
Chromosome 16CM028538.1=NC_052588.18
Chromosome 17CM028539.1=NC_052589.10
Chromosome 18CM028540.1=NC_052590.10
Chromosome 19CM028541.1=NC_052591.11
Chromosome 20CM028542.1=NC_052592.10
Chromosome 21CM028543.1=NC_052593.10
Chromosome 22CM028544.1=NC_052594.11
Chromosome 23CM028545.1=NC_052595.10
Chromosome 24CM028546.1=NC_052596.10
Chromosome 25CM028547.1=NC_052597.12
Chromosome 26CM028548.1=NC_052598.10
Chromosome 27CM028549.1=NC_052599.19
Chromosome 28CM028550.1=NC_052600.12
Chromosome 29CM028551.1=NC_052601.11
Chromosome 30CM028552.1=NC_052602.13
Chromosome 31CM028553.1=NC_052603.14
Chromosome 32CM028554.1=NC_052604.16
Chromosome 33CM028555.1=NC_052605.112
Chromosome 34CM028556.1=NC_052606.16
Chromosome 35CM028557.1=NC_052607.16
Chromosome 36CM028558.1=NC_052608.14
Chromosome 37CM028559.1=NC_052609.12
Chromosome 38CM028560.1=NC_052610.11
Chromosome 39CM028561.1=NC_052611.11
Chromosome WCM035081.1=NC_059535.119
Chromosome ZCM035082.1=NC_059536.10
unplacedn/an/an/a132

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule1,050,511,2392761,046,014,92890,563,9264090
Chromosome 1AllAssembled moleculeUnlocalized scaffolds196,369,742196,242,913126,829312196,154,486196,027,657126,829196,242,913196,242,91379,92043430000
Chromosome 2Assembled molecule149,940,1421149,780,671149,940,142280
Chromosome 3Assembled molecule110,406,8171110,405,217110,406,81790
Chromosome 4AllAssembled moleculeUnlocalized scaffolds90,624,98190,563,92661,05521190,623,26090,562,20561,05590,563,92690,563,92661,055880000
Chromosome 5AllAssembled moleculeUnlocalized scaffolds59,595,11959,353,219241,90061559,580,11959,338,219241,90059,353,21959,353,21966,524660000
Chromosome 6Assembled molecule36,041,924135,698,50936,041,92490
Chromosome 7AllAssembled moleculeUnlocalized scaffolds36,335,58236,265,83269,75021136,335,58236,265,83269,75036,265,83236,265,83269,750000000
Chromosome 8AllAssembled moleculeUnlocalized scaffolds29,671,38329,567,511103,87231229,526,87929,423,007103,87229,567,51129,567,51160,638880000
Chromosome 9AllAssembled moleculeUnlocalized scaffolds23,624,95323,494,135130,81831223,624,95323,494,135130,81823,494,13523,494,13594,312000000
Chromosome 10AllAssembled moleculeUnlocalized scaffolds20,451,34320,321,356129,98731220,397,22120,267,234129,98720,321,35620,321,35665,094440000
Chromosome 11Assembled molecule19,981,121119,946,75219,981,12140
Chromosome 12Assembled molecule20,129,920120,129,22020,129,92020
Chromosome 13Assembled molecule17,936,364117,833,61517,936,36440
Chromosome 14Assembled molecule15,370,873115,246,68915,370,87330
Chromosome 15Assembled molecule12,700,396112,700,39612,700,39600
Chromosome 16AllAssembled moleculeUnlocalized scaffolds1,763,2871,208,922554,3659181,761,2611,207,896553,3651,208,9221,208,92275,6451082000
Chromosome 17Assembled molecule10,459,299110,458,89910,459,29930
Chromosome 18Assembled molecule11,216,778111,196,62611,216,77840
Chromosome 19AllAssembled moleculeUnlocalized scaffolds10,311,64210,193,151118,49121110,311,34210,192,851118,49110,193,15110,193,151118,491220000
Chromosome 20Assembled molecule14,125,975114,125,37514,125,97540
Chromosome 21Assembled molecule6,842,59516,842,5826,842,59510
Chromosome 22AllAssembled moleculeUnlocalized scaffolds4,834,7414,783,20651,5352114,833,3414,781,80651,5354,783,2064,783,20651,535660000
Chromosome 23Assembled molecule6,197,48116,195,3986,197,48130
Chromosome 24Assembled molecule6,382,81916,382,6196,382,81910
Chromosome 25AllAssembled moleculeUnlocalized scaffolds3,136,3833,011,307125,0763123,047,2872,922,211125,0763,011,3073,011,30776,51911110000
Chromosome 26Assembled molecule5,297,96315,297,8635,297,96310
Chromosome 27AllAssembled moleculeUnlocalized scaffolds6,890,2296,402,218488,01110196,357,3645,869,353488,0116,402,2186,402,21854,70813130000
Chromosome 28AllAssembled moleculeUnlocalized scaffolds5,067,5064,978,24789,2593125,067,4064,978,14789,2594,978,2474,978,24755,678110000
Chromosome 29AllAssembled moleculeUnlocalized scaffolds431,919361,91870,001211431,319361,31870,001361,918361,91870,001220000
Chromosome 30AllAssembled moleculeUnlocalized scaffolds856,133380,481475,652413751,900277,248474,652295,388380,481295,388532000
Chromosome 31AllAssembled moleculeUnlocalized scaffolds1,920,1101,684,341235,7695141,919,8101,684,041235,7691,684,3411,684,34161,356330000
Chromosome 32AllAssembled moleculeUnlocalized scaffolds773,802255,904517,898716771,802254,404517,398203,613255,904117,347431000
Chromosome 33AllAssembled moleculeUnlocalized scaffolds4,223,6092,866,1861,357,423131123,038,2691,681,4461,356,8232,866,1862,866,186175,572862000
Chromosome 34AllAssembled moleculeUnlocalized scaffolds3,356,8763,049,188307,6887163,195,1782,887,490307,6883,049,1883,049,18851,20914140000
Chromosome 35AllAssembled moleculeUnlocalized scaffolds924,632321,869602,763716923,832321,669602,163261,329321,869143,587422000
Chromosome 36AllAssembled moleculeUnlocalized scaffolds543,478162,909380,569514541,478161,909379,569141,279162,909107,757422000
Chromosome 37AllAssembled moleculeUnlocalized scaffolds546,583373,902172,681312545,583372,902172,681373,902373,90290,149220000
Chromosome 38AllAssembled moleculeUnlocalized scaffolds577,136402,402174,734211575,836401,102174,734402,402402,402174,734440000
Chromosome 39AllAssembled moleculeUnlocalized scaffolds239,720192,48647,234211238,720191,48647,234192,486192,48647,234220000
Chromosome WAllAssembled moleculeUnlocalized scaffolds11,284,5199,109,9402,174,5792011910,920,8618,748,1822,172,6799,109,9409,109,940121,82628235000
Chromosome ZAssembled molecule86,044,486185,224,71286,044,4861270
unplacedAssembled molecule7,080,8781327,074,69662,656140